Neighbor Optimization MRE¶

This Jupyter notebook (05.02) details the analysis steps to optimize the nearest neighbor analysis.

THIS ANALYSIS STEP DOES NOT OUTPUT AN H5AD FILE.

Initialize Environment¶

First import all the necessary packages here:

InĀ [1]:
# Import necessary packages
import os
import scanpy as sc
import numpy as np
import pandas as pd
import anndata as ad
from datetime import datetime as dt

# Scanpy settings
sc.settings.verbosity = 3
sc.logging.print_header()

# Set working directory
os.chdir("/home/dalbao/2023-012-Runx3mutD8scRNA/AlbaoRunx3Manuscript/single_cell/02_optimization")

adata = "01_25-12-05-17-25_preprocessing_MRE.h5ad"
2025-12-05 22:27:57.336510: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: SSE4.1 SSE4.2 AVX AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
scanpy==1.9.5 anndata==0.10.2 umap==0.5.4 numpy==1.24.4 scipy==1.11.3 pandas==2.1.1 scikit-learn==1.3.1 statsmodels==0.14.0 igraph==0.11.2 louvain==0.8.1 pynndescent==0.5.10

Identify the starting directory. Get a timestamp for the run.

InĀ [2]:
# Determine work location
print("The work location for this notebook is: " + os.getcwd() + "\n")

# Get a timestamp for the start of the run
timestamp = dt.now()
print("This notebook was last run on " + timestamp.strftime("%y-%m-%d %H:%M") + "\n")
The work location for this notebook is: /blue/m.pipkin/dalbao/2023-012-Runx3mutD8scRNA/AlbaoRunx3Manuscript/single_cell/02_optimization

This notebook was last run on 25-12-05 22:28

The work directory is structured to contain a folder named "h5ad" which itself contains output from previous analysis steps. Import data from the latest analysis:

InĀ [3]:
# List items in outs folder
adata = ad.read_h5ad("../../h5ad/" + adata)

# Inspect AnnData
print(adata)
AnnData object with n_obs Ɨ n_vars = 28407 Ɨ 18505
    obs: 'experiment', 'group', 'timepoint', 'infection', 'cell_id', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'doublet_score', 'predicted_doublet', 'scDblFinder_score', 'scDblFinder_class', 'gem', 'QC', 'n_genes', 'S_score', 'G2M_score', 'phase'
    var: 'mt', 'ribo', 'n_cells_by_counts-gem1', 'mean_counts-gem1', 'log1p_mean_counts-gem1', 'pct_dropout_by_counts-gem1', 'total_counts-gem1', 'log1p_total_counts-gem1', 'n_cells_by_counts-gem2', 'mean_counts-gem2', 'log1p_mean_counts-gem2', 'pct_dropout_by_counts-gem2', 'total_counts-gem2', 'log1p_total_counts-gem2', 'n_cells', 'n_counts', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'group_colors', 'hvg', 'log1p', 'pca'
    obsm: 'X_pca'
    varm: 'PCs'
    layers: 'counts', 'soupX_counts'

Optimize Nearest Neighbors¶

Write a function to automate iteration of nearest neighbor analysis:

InĀ [4]:
# Define a function to automate the iteration of different neighbor values, holding PC constant.
def iterate_neighbors(adata_local, pcs = 25, neighbors = 10, min = 0, max = 11):
    # Loop over different nearest neighbor values based on provided min and max values
    for index in range(min, max):
        # Calculate nearest neighbors with n_neighbors of neighbors + index
        adata_mod = sc.pp.neighbors(adata_local, n_neighbors = neighbors + index, n_pcs = pcs, copy = True)
        
        # Do leiden clustering from neighborhood graph
        sc.tl.leiden(adata_mod)
        
        # Initialize the PAGA
        sc.tl.paga(adata_mod)
        sc.pl.paga(adata_mod, title = "neighbor " + str(neighbors + index) + " pcs " + str(pcs))

        # Do a UMAP based on initialized PAGA graph
        sc.tl.umap(adata_mod, init_pos='paga')

        # Plot UMAP annotated by leiden clusters and original identity
        sc.pl.umap(adata_mod, color = "group", title = "neighbor " + str(neighbors + index) + " pcs " + str(pcs))
        sc.pl.umap(adata_mod, color = "leiden", title = "neighbor " + str(neighbors + index) + " pcs " + str(pcs))

        # Get leiden clusters and original identities
        obs_df = sc.get.obs_df(adata_mod, ["group", "leiden"])
        # Print tapply
        print(obs_df.groupby("group").value_counts().unstack())

        del(adata_mod) # Cleanup
        
    # End of loop
    
    del(adata_local)
            
# End of function

25 PCs, neigbhor 3 to 18¶

InĀ [5]:
iterate_neighbors(adata, pcs = 25, neighbors = 3, min = 0, max = 18)
computing neighbors
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:20)
running Leiden clustering
    finished: found 51 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:02)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3    4    5    6    7    8    9  ...  41  42  43  \
group                                                        ...               
Base       6     1     6   20  377  393   20  523  119  528  ...  26   2   0   
Naive      0     0     0    0    0    0    0    0    0    0  ...   0   0   0   
Null       0     0    23    1  357  283   47  282  618  339  ...  18   5   0   
WT        25  1545    33  136   46   71   21   82   46   35  ...  16   0   0   
d5         3     2     2    1   23   19    6    4    2    6  ...   1   0  19   
d8         6     0     0    5  242   95    7   51   64   84  ...   1   0   0   
dAD        8     0  1315   45   46   94  902   63  123   29  ...  13  24   0   
dID     1679     9    17   33   62   75   28   47   73   42  ...  13   3   5   
dVWRPY    17    42    67  979   37   74   61   38   40   20  ...   5   0   0   

leiden  44  45  46  47  48  49  50  
group                               
Base     0   0   0   0   1   0   0  
Naive    0   0   0   0   0   3   0  
Null     0   0   0   1   2   0   2  
WT       0   0   1   0   0   0   0  
d5       0   6   0   0   0   0   0  
d8       0   0   0   0   0   0   0  
dAD     17   0   0   2   0   0   1  
dID      0   0   0   0   0   0   0  
dVWRPY   1   1   3   1   0   0   0  

[9 rows x 51 columns]
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 25 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5    6    7    8    9  ...   15   16  \
group                                                          ...             
Base       9   679     3    20    11  460  546  742  584   19  ...  265    0   
Naive      0     0     0     0     0    0    0    0    0    0  ...    1  542   
Null      27  1214     0     0     5  828  374  557  397    7  ...  118    0   
WT        45    85  2295    37   244   65  177   69   77  673  ...   66    0   
d5         3    15     3     6     7    9   34    7   21   17  ...   12    0   
d8         1   129     0    14     4  102  137  101  305    4  ...  194    0   
dAD     2484   219     1     8    78  120  134   80   63   37  ...   32    0   
dID       27   121    14  2114    60  130  211   59   90   63  ...  114    0   
dVWRPY    97    77    59    36  1708   67  108   38   42  755  ...   44    0   

leiden   17  18  19  20  21  22  23  24  
group                                    
Base      8  33  35  29   3   0   9   1  
Naive     0   0   0   0   1   0   0   0  
Null      1  33  17  38  11   0  21   0  
WT      279  76  30  29   8   0   2   0  
d5        1   6   4   2  39  94   1   0  
d8        3  19   5   1  11   0  10   0  
dAD       5  28   9  20  16   0   4   0  
dID      12  27  67  21  11   0   7   1  
dVWRPY  110  56  21   8  15   1   7   2  

[9 rows x 25 columns]
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 19 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3     4    5     6    7    8     9   10   11   12  \
group                                                                           
Base     941     5  824    10    21  797    15  486  659     4   17   32  124   
Naive      0     0    0     0     0    1     0    0    0     0    0    0    0   
Null    1485     1  608     7     2  483    49  851  807    13    7   42   74   
WT       168  2928  244    43   344  104    36   59   92    24  248   30  275   
d5        19     7   36     6    10   34     3   11    6     1   13  746   22   
d8       148     0  174     9    11  514     3  126   64     0   13   79   18   
dAD      230     4  186     9    87   90  1760  132   75  1531   45   30   66   
dID      156    22  230  2374    65  170    30  144   76    14   43   54  219   
dVWRPY    99   116  197    41  1936   61    78   80   42    47  719   42  163   

leiden   13   14  15  16  17  18  
group                             
Base    205    0  31   2  23   1  
Naive     0  542   0   1   0   0  
Null     87    0  17  11  21   0  
WT      124    0  30   8  14  59  
d5        5    0   4  45   1   0  
d8       33    0   5  11   1   0  
dAD      59    0   9  13  22   3  
dID     316    0  63  11  22   2  
dVWRPY   44    0  21  16   9  20  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 18 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7    8    9   10   11   12  \
group                                                                           
Base     953     5     6   621    26     7  968  584  598   18   22  189   12   
Naive      0     0     0     0     0     0    0    1    0    0    0    0    0   
Null    1574     0    27  1328     7     0  615  330  426    6   36   74   35   
WT       147  2915    42   114   391    43   77  169   94  247   26  131   20   
d5        17     6     3    20     8     7    9   36   25   15  749    5    7   
d8       164     0     3   155    10    12  136  192  379   11   75   34    7   
dAD      203     4  2577   218    85     8   75   93   81   32   29   54  790   
dID      155    29    27   185    87  2240   77  240  124   53   49  454   24   
dVWRPY    91    98    83    99  1943    31   47  135   38  835   47   45   80   

leiden   13   14  15  16  17  
group                         
Base    129    0  32   3  24  
Naive     0  542   0   1   0  
Null     54    0  17  12  24  
WT      359    0  28   8  19  
d5       16    0   3  42   1  
d8       13    0   5  12   1  
dAD      63    0  10  13  16  
dID     173    0  60  12  22  
dVWRPY  112    0  21  16  10  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 19 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3    4     5     6     7     8    9    10   11  \
group                                                                        
Base     797   487    10  749  633     1    25     3    13  905    13  167   
Naive      0     0     0    0    0     0     0     0     0    0     0    1   
Null    1263  1217     2  679  576     0     8    21     2  514    42   37   
WT       124    90    42   88  210  2151   224    26  1043   67    42  269   
d5        15    16     5   28   39     3     8     1    13    9     5    6   
d8        98   145    12  445  197     0     8     2    10   95     5   58   
dAD      136   196     8   95  164     0    97  1898    24   51  1495   29   
dID      124   159  2281  132  244     4    62    17    61   58    31   81   
dVWRPY    64    90    32   49  172    27  1615    57   772   46    77  510   

leiden   12   13   14   15  16  17  18  
group                                   
Base     24  196  116    0  31   3  24  
Naive     0    0    0  542   0   1   0  
Null     40   79   34    0  17  11  23  
WT       26  107  273    0  26   8  14  
d5      755    6   15    0   4  40   1  
d8       73   34    9    0   5  12   1  
dAD      31   51   37    0   9  13  17  
dID      51  450  175    0  55  11  15  
dVWRPY   47   41   87    0  21  16   8  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 17 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4     5     6    7    8    9   10   11   12  \
group                                                                           
Base      11     8    18   827  824     9  1158  650  327   21  209   11   64   
Naive      0     0     0     0    1     0     0    0    0    0    0    0    0   
Null      38     0     3  1320  630     3   851  625  878   36   93    4   34   
WT        56  3073   426   140  227    39   111   88   79   24  130  170  217   
d5         6     8    10    12   36     4     9   27   19  766    7    8   16   
d8         4     1    15   131  224    14   149  397  128   80   35    4    9   
dAD     3245     7    86   167  265     9    98   92  191   29   61   20   43   
dID       33    25    87   132  251  2445    95  114  173   45  326   34  169   
dVWRPY   102   118  2228    75  221    33    50   43  102   46   44  540   84   

leiden   13  14  15  16  
group                    
Base      0  32   2  26  
Naive   542   0   1   0  
Null      0  17  11  22  
WT        0  26   8  16  
d5        0   4  36   1  
d8        0   5  12   1  
dAD       0   9  13  16  
dID       0  55  11  16  
dVWRPY    0  21  16   8  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 17 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4     5     6    7    8    9   10   11   12  \
group                                                                           
Base      10     3   868   570  760    15    22  808  776   18   24  200   63   
Naive      0     0     0     0    1     0     0    0    0    0    0    0    0   
Null      33     0  1419  1320  581     4     7  609  412    6   30   71   21   
WT        53  2937   139   106  215    38   348  103   85  365   25  118  249   
d5         5     7    14    17   40     7     8   34   12   13  751    3   16   
d8         1     0   128   174  242    16     6  440   65   10   67   34    8   
dAD     3214     1   164   206  324     7    79   95   59   50   28   56   30   
dID       33    16   157   199  268  2484    83  113   44   56   41  300  134   
dVWRPY    96    87    77    94  206    33  1896   51   40  942   45   44   74   

leiden   13  14  15  16  
group                    
Base      0  31   2  27  
Naive   542   0   1   0  
Null      0  17  11  24  
WT        0  26   8  15  
d5        0   4  36   2  
d8        0   5  12   1  
dAD       0   9  13  16  
dID       0  56  11  16  
dVWRPY    0  21  16   9  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 17 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6     7     8    9   10   11  \
group                                                                         
Base     887  1091   687  1008     5    19    11    18     5   23   14  167   
Naive      0     0     0     1     0     0     0     0     0    0    0    0   
Null    1380   862  1351   702    26     6     5     3     0   35   22   42   
WT       138   102   100   219    39   349    39  1539  1799   25   17  299   
d5        16    31    20    43     1    11     6    19     1  755    4   17   
d8       131   477   184   244     0     7    15     6     0   79    3    9   
dAD      153   104   209   165  2630    88     6    27     1   30  803   41   
dID      149   126   187   253    24    84  2515    46     7   43   12  190   
dVWRPY    75    53    99   194    80  2141    44   743    40   44   51   76   

leiden   12   13  14  15  16  
group                         
Base    201    0  32  27   2  
Naive     0  542   0   0   1  
Null     79    0  17  24  11  
WT      109    0  27  21   8  
d5        5    0   4   2  34  
d8       36    0   5   1  12  
dAD      56    0   9  16  13  
dID     289    0  59  16  11  
dVWRPY   44    0  21  10  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:07)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7    8    9  10  11  12  13
group                                                                         
Base    1278  1521    12    12    18    52  996   25  212    0  11  31  27   2
Naive      0     0     0     0     0     0    1    0    0  542   0   0   0   1
Null    2438  1267     1    32     7     8  606   40   94    0  19  17  25  11
WT       285   321  3265    59   447    59  107   30  124    0  75  27  23   8
d5        30    45    12     8    12     7   34  768    6    0   8   4   1  34
d8       251   298     1     2    12    41  460   84   36    0   6   5   1  12
dAD      277   405     4  3279   101    11  115   43   55    0  21  10  17  13
dID      291   362    41    35    93  2516  146   45  323    0  72  56  20  11
dVWRPY   158   247   242   116  2672    43   57   48   47    0  54  21  10  16
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6     7    8    9   10   11  \
group                                                                        
Base    1409  1711     5    19   582    35     3    75   30  203   63    0   
Naive      0     0     0     0     0     0     0     1    0    0    0  542   
Null    1211  1532    23     7  1566     9     0    13   38   88   23    0   
WT       281   185    50   405   128    38  2188  1096   31  122  248    0   
d5        48    37     3    10    12     5     1    18  768    8   16    0   
d8       281   536     0    10   179    37     0    13   89   39    7    0   
dAD      655   160  3024    96   210    10     1    21   37   67   30    0   
dID      349   171    30    99   219  2505     5    68   47  308  121    0   
dVWRPY   263    94    88  2451   111    42    40   429   52   44   70    0   

leiden  12  13  14  
group               
Base    32  27   3  
Naive    0   0   1  
Null    17  26  12  
WT      27  23   8  
d5       4   1  38  
d8       5   1  12  
dAD     10  17  13  
dID     59  18  12  
dVWRPY  21  10  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:13)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7     8    9   10   11  \
group                                                                       
Base    1409  1275     8     4    12    42  826  245    12   30  188   87   
Naive      1     0     0     0     0     0    0    0     0    0    0    0   
Null    1166  1744     1    29     6    12  540  865     1   37   74   38   
WT       267   157  3145    48    46   458   97   57   129   33  123  216   
d5        47    20     5     2     8    22   25   10     2  770    4   15   
d8       271   178     0     1    18    18  453  126     0   84   33    9   
dAD      588   174     3  3054     9    86   98  113    31   39   57   60   
dID      329   136    27    30  2540    83  108   99    38   51  281  206   
dVWRPY   240    84   146    97    39  1726   43   66  1066   54   42   81   

leiden   12  13  14  15  
group                    
Base      0  31  26   2  
Naive   542   0   0   1  
Null      0  17  24  11  
WT        0  27  19   8  
d5        0   4   1  34  
d8        0   5   1  12  
dAD       0  10  16  13  
dID       0  55  17  11  
dVWRPY    0  21  11  15  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5     6     7    8    9   10   11  12  \
group                                                                           
Base    1431  1383     5    26    14  936    41     3   30  192    0   76  32   
Naive      0     1     0     0     0    0     0     0    0    0  542    0   0   
Null    2414  1302    25     7     4  623     8     1   37   62    0   28  17   
WT       226   278    46   310    43  104  1381  2040   31  113    0  201  27   
d5        26    47     1     8     8   32    20     0  768    4    0   16   4   
d8       272   274     0     7    13  484    13     0   85   35    0    7   5   
dAD      273   654  3023    97     6  103    36     1   39   52    0   28   9   
dID      270   337    25    87  2497  135    71     7   50  309    0  138  54   
dVWRPY   136   263    81  2091    37   49   856    44   49   42    0   34  21   

leiden  13  14  
group           
Base    26   2  
Naive    0   1  
Null    26  11  
WT      22   8  
d5       0  35  
d8       2  12  
dAD     17  13  
dID     20  11  
dVWRPY  12  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:06)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:10)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10   11  12  \
group                                                                           
Base    1265    17  1284     9   664    24    18  557   25  200   72    0  32   
Naive      1     0     0     0     0     0     0    0    0    0    0  542   0   
Null     959     3  1110    26  1620     8     5  641   41   71   27    0  17   
WT       291  3304   129    49   115   381    46   98   29  118  212    0  28   
d5        57    15    31     2    15     8     7   12  757    5   13    0   4   
d8       276     1   501     1   209     9    20   52   80   35    7    0   5   
dAD      440     9   147  3202   201   104     6   78   39   54   32    0   9   
dID      343    49   154    23   185    99  2537   75   43  279  138    0  55   
dVWRPY   371   406    62    91   104  2410    41   48   55   47   48    0  21   

leiden  13  14  
group           
Base    27   3  
Naive    0   1  
Null    26  11  
WT      22   8  
d5       2  41  
d8       1  12  
dAD     17  13  
dID     19  12  
dVWRPY  11  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:07)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:10)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10   11  \
group                                                                       
Base    1269  1176    17     5  1027    17     2  210   26   28  180  180   
Naive      1     0     0     0     0     0     0    0    0    0    0    0   
Null     963  1862     2    16   762     4     0  738   13   37   60   58   
WT       283   149  1529    44   101    42  1989   36  101   30  357  110   
d5        50    21    19     0    32     7     3    6    4  768   17    3   
d8       274   198     6     0   480    12     0   87    5   81   15   33   
dAD      611   204    51  3029   115     5     0   93   67   36   48   53   
dID      336   162    82    25   138  2449     8   95   52   47  210  308   
dVWRPY   403    87  1802    80    60    31   106   40  901   47   85   39   

leiden   12  13  14  15  
group                    
Base      0  32  26   2  
Naive   542   0   0   1  
Null      0  17  22  11  
WT        0  29  22   8  
d5        0   4   0  35  
d8        0   5   1  12  
dAD       0   9  17  13  
dID       0  55  33  11  
dVWRPY    0  21  13  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:06)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:15)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9  10  11  12
group                                                                      
Base      13  1200  1431     9  1075    14   161   28  206    0  32  26   2
Naive      0     0     1     0     0     0     0    0    0  542   0   0   1
Null       3  2214  1180    28   901     3    52   42   87    0  17  27  11
WT      3504   156   291    50   123    46   450   29  124    0  28  21   8
d5        22    21    48     2    34     8    22  767    5    0   4   1  35
d8         4   246   305     0   481    20    17   82   35    0   5   2  12
dAD       38   226   417  3271   133     6   119   39   63    0   9  17  13
dID       63   213   347    29   147  2506   262   44  315    0  55  19  11
dVWRPY  1675   110   361    89    57    45  1254   48   44    0  21  11  16
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:06)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:13)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:15)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10   11  12  \
group                                                                           
Base    1137  1358    10     2    21  1142    18   29  222   15  182    0  32   
Naive      0     1     0     0     0     0     0    0    0    0    0  542   0   
Null    2195  1175    24     0     5   922     5   37   78    4   68    0  17   
WT       151   253    53  2979   457   120    43   31  314  253  119    0  27   
d5        22    47     2     4    13    30     7  770   18   12    5    0   4   
d8       240   299     1     0     9   486    16   85   18    6   31    0   5   
dAD      248   268  3377     1    94   131     9   37   67   27   53    0   9   
dID      203   334    29    15    73   132  2599   46  237   37  222    0  54   
dVWRPY   118   179   100    95  2362    57    34   47   87  558   44    0  21   

leiden  13  14  
group           
Base    27   2  
Naive    0   1  
Null    24  11  
WT      22   8  
d5       1  34  
d8       1  12  
dAD     17  13  
dID     19  11  
dVWRPY  13  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:07)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:15)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6     7    8    9   10   11  \
group                                                                        
Base    1240  1322     6     6  1133    10    30    15   29  167  180    0   
Naive      0     1     0     0     0     0     0     0    0    0    0  542   
Null    2330  1178     1    21   821     4    10     5   37   47   61    0   
WT       157   253  2453    46   117    46   154  1108   30  301  114    0   
d5        23    48     7     2    32     8    10    15  763   17    5    0   
d8       257   294     2     1   491    11     5     5   84    8   33    0   
dAD      249   400    24  3229   125     6   123    15   40   45   57    0   
dID      226   336    37    24   147  2527    67    45   44  200  276    0   
dVWRPY   116   182  1231    79    68    39  1412   400   51   67   43    0   

leiden  12  13  14  
group               
Base    31   2  26  
Naive    0   1   0  
Null    17  11  22  
WT      26   8  17  
d5       4  35   0  
d8       5  12   1  
dAD      9  13  16  
dID     54  11  17  
dVWRPY  21  16   6  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:06)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:13)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:16)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6     7    8    9   10   11  \
group                                                                        
Base    1282  1234    11  1179    11     0    29    10   29  150  202    0   
Naive      0     1     0     0     0     0     0     0    0    0    0  542   
Null    2319  1222    20   766     5     0     6     4   38   48   86    0   
WT       163   222    49   138    40  2549   778   355   32  336  115    0   
d5        21    50     1    28     7     3    20     7  768   17    8    0   
d8       257   311     0   469    16     0    10     4   81    9   34    0   
dAD      254   431  3220   130     7     0    93    40   37   43   58    0   
dID      226   338    30   133  2536     7    74    45   47  203  288    0   
dVWRPY   132   155   101    61    30    62  1335  1622   55   87   44    0   

leiden  12  13  14  
group               
Base    31  27   2  
Naive    0   0   1  
Null    17  23  11  
WT      27  18   8  
d5       4   1  34  
d8       5   1  12  
dAD      9  16  13  
dID     54  19  11  
dVWRPY  21  10  16  
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())

30 PCs, neigbhor 3 to 18¶

InĀ [6]:
iterate_neighbors(adata, pcs = 30, neighbors = 3, min = 0, max = 18)
computing neighbors
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 48 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:02)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3     4    5    6     7    8    9  ...  38  39  \
group                                                          ...           
Base       7     2  588    20     5  429   14     5  318   19  ...   1  33   
Naive      0     0    0     0     0    1    0     0    0    0  ...   1   0   
Null      19     1  576     2     1  295    9     0  310   29  ...  11   7   
WT        26  1622   99    27   171  105  206  1024   61   21  ...   7   7   
d5         1     7   23     4     6   42   14     2   16    3  ...  20   3   
d8         1     0   88    10     0   95   16     0  240    1  ...  12   3   
dAD     1914     0   67     2    30   83   57     0   39  787  ...  12   2   
dID        8    18   84  1409    41   98   57    26   66   21  ...  11  28   
dVWRPY    68    95   43    20  1137   71  755    44   27   42  ...  15   4   

leiden  40  41  42  43  44  45  46  47  
group                                   
Base    17   1   0   0   3   3   0   0  
Naive    0   0   0   0   0   0   3   0  
Null    12   1   0   0   0   0   0   2  
WT      17   2   0   0   1   0   0   0  
d5       0   0   8   7   0   0   0   0  
d8       1   0   0   0   0   0   0   0  
dAD     10   0   0   0   0   0   0   0  
dID     15   0   0   0   0   0   0   1  
dVWRPY   6   4   0   1   0   0   0   0  

[9 rows x 48 columns]
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 26 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5     6    7    8    9  ...   16   17  \
group                                                          ...             
Base      11     4   816     2  521  836    16  291  509   12  ...  173  191   
Naive      0     0     0     0    0    0     0    0    0    0  ...    0    0   
Null       7     0  1031    21  515  564     4  802  387    4  ...   74  107   
WT        37  2279   109    31  144   58   212   62   77  934  ...  120  221   
d5         5     4    26     3   41   13     6    2   20   13  ...    3   12   
d8        17     0   111     0  134  143    11   96  277    5  ...   33   18   
dAD        8     1    99  2051  153   65    40  166   60    8  ...   51   45   
dID     2276    14    78    15  163   68    52  105   87   64  ...  332  194   
dVWRPY    27    73    42    48  116   31  1305   55   36  302  ...   59   34   

leiden   18   19  20  21  22  23  24  25  
group                                     
Base      0    2  14  31  29   2   0   0  
Naive   542    0   0   0   0   1   0   0  
Null      0  115   8  17  23  11   0   0  
WT        0    3  49  27  35   8   0   0  
d5        0    1   1   4   1  41  98   7  
d8        0    3   4   5   1  12   0   0  
dAD       0   44  22  10  17  13   0   0  
dID       0    9  24  49  21  11   0   0  
dVWRPY    0    3  51  21  12  15   0   1  

[9 rows x 26 columns]
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 20 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5    6     7     8     9   10   11  \
group                                                                        
Base       8   862    25  1098    14  675  446    16    24     0  353  224   
Naive      0     0     0     0     0    0    0     0     0     0    0    0   
Null       0  1583    10   736    46  561  981     3     9    12  249  108   
WT      3106   132    39    90    45  192   82   268   240    13   54  135   
d5        11    23     7    17     7   47   11     3    17     1   14    8   
d8         3   173    28   180     5  179  114     5     9     0  253   38   
dAD        3   206    10   110  2143  175  151    73    87  1094   48   75   
dID       41   157  2399   115    38  213  135    60    76     4   50  320   
dVWRPY   175    80    20    52    95  127   82  1501  1257    33   26   57   

leiden   12   13   14   15  16  17  18   19  
group                                        
Base     27   97  264    0  34  28   2    0  
Naive     0    0    1  542   0   0   1    0  
Null     41   36  137    0  18  24  11    0  
WT       31  294   36    0  29  36   8    0  
d5      623   14    9    0   4   1  41  111  
d8       82   12  110    0   5   1  12    0  
dAD      41   54   41    0  10  17  13    0  
dID      51  209   62    0  45  25  11    0  
dVWRPY   62   88   26    0  20  14  15    1  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 18 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4     5     6     7     8    9   10   11  \
group                                                                        
Base    1108    17    25  931     9  1002     4   483    18   34  203  141   
Naive      0     0     0    0     0     0     0     0     0    0    0    0   
Null    1707     2     5  739     5   697    19  1062    42   44  105   32   
WT       175  3158   426  223    39    95    34    79    36   34  126  254   
d5        23    15    11   47     6    30     3    10     5  750    4   13   
d8       194     4     7  182    11   427     0   124     7   84   38   10   
dAD      191     5    92  185     8    96  2346   191  1012   42   61   40   
dID      180    62    74  234  2433   122    12   154    33   52  309  186   
dVWRPY   104   332  2485  197    35    50    80    75   116   61   45   35   

leiden   12   13  14  15  16  17  
group                             
Base      0  147  15  32  26   2  
Naive   542    1   0   0   0   1  
Null      0   35  17  17  26  11  
WT        0   20  69  29  25   8  
d5        0    4   2   4   1  41  
d8        0   96   7   5   1  12  
dAD       0   18  24  10  17  13  
dID       0   52  27  51  19  11  
dVWRPY    0   14  53  20  14  15  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 17 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4     5    6     7    8    9   10   11   12  \
group                                                                           
Base    1036    10    10  883     7    21  907    20  658  231   30  209  114   
Naive      0     0     0    1     0     0    0     0    0    0    0    0    0   
Null    1780    51     1  781     5     8  584     5  430  686   47  104   30   
WT       164    51  3008  220    31   261   65   352   88   50   31  130  318   
d5        18     4     7   36     4     5   10    17   22    6  767    4   19   
d8       193     3     2  232    12     6  141    15  380   83   77   39    7   
dAD      209  3242     2  252     6    89   87    80   82  117   37   60   48   
dID      176    32    29  271  2425    62   78    67  120  124   51  308  190   
dVWRPY    83   101   113  183    27  1561   46  1286   38   71   45   44   84   

leiden   13  14  15  16  
group                    
Base      0  31  27   3  
Naive   542   0   0   1  
Null      0  17  24  12  
WT        0  29  24   8  
d5        0   4   1  45  
d8        0   5   1  13  
dAD       0  10  17  13  
dID       0  41  24  13  
dVWRPY    0  20  14  15  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7     8    9   10   11  \
group                                                                       
Base    1222     9  1194    24    20     6  783  550     3   25  213   87   
Naive      0     0     0     0     0     0    0    1     0    0    0    0   
Null    2038    48  1378     5     4     4  495  369     0   44  102   25   
WT       195    52   154   386  1747    27   99  156  1562   27  102  269   
d5        22     4    19     9    18     6   29   29     0  762    5   16   
d8       216     3   177    10     7    14  490  147     0   78   37   11   
dAD      256  3299   209    98    23     7   98  170     1   39   70   41   
dID      212    34   217    98    65  2450  131  196     2   47  308  169   
dVWRPY   113   102   130  2158   769    26   41  145    48   45   42   67   

leiden   12  13  14  15  
group                    
Base      0  31   2  28  
Naive   542   0   1   0  
Null      0  17  12  24  
WT        0  27   8  19  
d5        0   4  45   1  
d8        0   5  13   1  
dAD       0  10  13  17  
dID       0  49  13  20  
dVWRPY    0  20  15  10  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7    8    9   10  11  12  \
group                                                                         
Base    1480  1379    10     5    22    10  846   29  203  151    0  31  27   
Naive      0     0     0     0     0     0    1    0    0    0  542   0   0   
Null    2533  1209     3    28     5     5  552   44   95   38    0  17  24   
WT       234   296  3243    44   423    34  107   32  122  236    0  27  24   
d5        24    50    10     2    13     6   28  763    5   19    0   4   1   
d8       283   278     3     2     9    25  457   83   36   14    0   5   1   
dAD      280   616     6  3057    88     9  106   39   59   51    0   9  18   
dID      271   337    42    28    84  2481  114   51  306  196    0  50  38   
dVWRPY   136   397   288   111  2502    34   51   47   45   64    0  21  20   

leiden  13  
group       
Base     4  
Naive    1  
Null    12  
WT       8  
d5      44  
d8      13  
dAD     13  
dID     13  
dVWRPY  15  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7    8    9   10  11  12  \
group                                                                         
Base    1466  1519    10     8    24    10  805   30  189    0   74  31  27   
Naive      0     0     0     0     0     0    1    0    0  542    0   0   0   
Null    2490  1329     3    44     7     5  475   42   93    0   25  17  23   
WT       238   290  3294    55   417    32   97   31  113    0  203  27  25   
d5        25    59    11     2    11     7   27  759    4    0   16   4   1   
d8       285   299     1     1    12    18  445   84   36    0    9   5   1   
dAD      301   411     4  3238   119     5  103   39   62    0   29   9  18   
dID      291   365    45    28   103  2453  118   51  327    0  128  55  34   
dVWRPY   137   306   270   105  2655    29   48   46   45    0   40  21  13   

leiden  13  
group       
Base     4  
Naive    1  
Null    12  
WT       8  
d5      43  
d8      13  
dAD     13  
dID     13  
dVWRPY  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6     7    8    9   10  11  12  \
group                                                                           
Base    1475  1659     6   621     4    16    13   126   31  182    0  30  27   
Naive      1     0     0     0     0     0     0     0    0    0  542   0   0   
Null    1175  1460    26  1689     0     3     7    31   47   66    0  17  24   
WT       304   182    40   104  2795   763    37   371   31  104    0  29  24   
d5        63    37     0    17     4    16     7    16  759    4    0   4   2   
d8       320   521     2   174     0    12    23     9   91   35    0   5   2   
dAD      607   163  3016   221     2    53     8   130   38   53    0  10  18   
dID      356   144    27   208    23    63  2488   228   51  305    0  55  34   
dVWRPY   322    76    69    79    60  1816    30  1107   47   40    0  21  14   

leiden  13  14  
group           
Base     5   2  
Naive    0   1  
Null     9  11  
WT      38   8  
d5       1  39  
d8       3  12  
dAD     19  13  
dID     18  11  
dVWRPY  35  15  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9  10  11  12  \
group                                                                         
Base    1524  1172     6     7    30  1167    12   33  180    0  32  26   5   
Naive      0     1     0     0     0     0     0    0    0  542   0   0   0   
Null    2439  1084     1    40    10   794     6   44   82    0  18  25  11   
WT       325   305  3330    57   406   127    36   35  119    0  28  27  27   
d5        30    68    11     1    13    28     9  752    7    0   4   3   1   
d8       278   255     0     2     8   503    18   89   34    0   5   1   4   
dAD      275   410     4  3250   126   126     8   39   54    0  10  18  18   
dID      337   398    40    26   108   143  2481   49  308    0  56  34  20   
dVWRPY   139   257   231   105  2734    55    32   47   46    0  21  16  32   

leiden  13  
group       
Base     3  
Naive    1  
Null    11  
WT       8  
d5      42  
d8      12  
dAD     13  
dID     11  
dVWRPY  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:09)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6     7    8    9   10  11  12  \
group                                                                           
Base    1253  1296    22     9  1295    38    10     1   31  179    0  31  25   
Naive      0     1     0     0     0     0     0     0    0    0  542   0   0   
Null    2291  1133     4    30   902    12     5     0   42   87    0  17  23   
WT       243   320  2143    45   130   372    31  1282   33  102    0  26  35   
d5        23    64    21     1    34    10     7     1  764    4    0   3   2   
d8       236   262     8     2   528     8    22     0   88   34    0   5   2   
dAD      267   570    40  3066   145   102     7     1   39   57    0  10  18   
dID      274   389    69    24   157   153  2466     7   48  307    0  53  37   
dVWRPY   103   269  1058    94    62  1896    25    45   48   40    0  21  21   

leiden  13  14  
group           
Base     5   2  
Naive    0   1  
Null     8  11  
WT      60   8  
d5       1  34  
d8       2  12  
dAD     16  13  
dID     16  11  
dVWRPY  33  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6     7    8    9   10  11  12  \
group                                                                           
Base    1470  1220     6  1160    19    10    33     1   31  178    0  32   9   
Naive      0     1     0     0     0     0     0     0    0    0  542   0   0   
Null    2482  1039    32   808     4     4     8     0   42   80    0  18  11   
WT       274   336    45   113  1446    29   281  2072   33  101    0  26  39   
d5        23    63     2    31    21     8     8     0  768    4    0   4   1   
d8       281   243     3   502    10    17     6     0   91   34    0   5   4   
dAD      285   347  3269   136    43     5   106     1   40   56    0  10  22   
dID      327   402    25   139    64  2474    91    11   48  306    0  53  26   
dVWRPY   121   248    73    55  1176    25  1801    45   46   41    0  21  43   

leiden  13  14  
group           
Base    26   2  
Naive    0   1  
Null    26  11  
WT      27   8  
d5       1  35  
d8       1  12  
dAD     18  13  
dID     34  11  
dVWRPY  21  15  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6     7    8    9   10  11  12  \
group                                                                           
Base    1361  1182     4  1263    22    16    78     1   28  175    0  32  28   
Naive      0     1     0     0     0     0     0     0    0    0  542   0   0   
Null    2446  1044    32   824     5     7    18     0   43   83    0  17  26   
WT       212   256    48   121  1327    29   487  2131   34   98    0  28  26   
d5        24    55     0    33    26     8    12     0  767    4    0   3   2   
d8       248   231     0   548    10    18    10     0   91   33    0   5   1   
dAD      254   485  3138   145    68     5   103     1   41   56    0  10  19   
dID      258   343    23   167    82  2484   189     7   49  298    0  50  35   
dVWRPY   115   218    93    60  1377    24  1632    37   48   41    0  21  23   

leiden  13  14  
group           
Base     2   5  
Naive    1   0  
Null    11   9  
WT       8  25  
d5      34   1  
d8      12   2  
dAD     13  13  
dID     11  15  
dVWRPY  16  26  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7     8    9   10   11  12  \
group                                                                           
Base    1549  1227     4     4     8    19  796   15   304   30  174    0  31   
Naive      0     0     0     0     0     0    1    0     0    0    0  542   0   
Null    1619  1077    28     1     5     6  486    5  1174   40   62    0  17   
WT       330   269    44  2582    24   269   97  939    66   30   96    0  28   
d5        30    58     0     1     8     6   31   20    11  754    4    0   3   
d8       225   251     0     0    19     4  474    6    82   92   33    0   5   
dAD      221   559  3056     2     5    97  103   38   118   39   54    0   9   
dID      304   331    21    14  2521    78  109   64   134   47  292    0  49   
dVWRPY   129   239    90    76    26  1983   40  944    34   47   41    0  21   

leiden  13  14  15  
group               
Base     6  27   3  
Naive    0   0   1  
Null     9  25  11  
WT      30  18   8  
d5       1   2  40  
d8       4   2  12  
dAD     20  17  13  
dID     19  17  11  
dVWRPY  37   9  15  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5     6     7    8    9   10   11  12  \
group                                                                           
Base    1318  1483     5    10    25  987     0    22   31  183   72    0  32   
Naive      0     1     0     0     0    0     0     0    0    0    0  542   0   
Null    2379  1286    27     4     8  656     0     4   43   86   21    0  17   
WT       217   282    45    29   300  100  2311  1121   32   98  237    0  27   
d5        19    54     0     8     7   32     0    23  766    4   17    0   3   
d8       253   300     0    22     5  473     0     8   89   34    7    0   5   
dAD      253   544  3117     7   117  111     1    41   39   53   27    0   9   
dID      263   362    23  2526    90  116     6    68   51  276  144    0  41   
dVWRPY   114   239    85    23  2021   53    43   966   46   40   49    0  21   

leiden  13  14  
group           
Base    27   2  
Naive    0   1  
Null    23  11  
WT      23   8  
d5       1  35  
d8       1  12  
dAD     19  13  
dID     34  11  
dVWRPY  15  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7    8    9   10  11  12  \
group                                                                         
Base    1627  1401     5     2    22     9  835   23   29  179    0  32   2   
Naive      0     0     0     0     0     0    1    0    0    0  542   0   1   
Null    2593  1267    31     0     6     5  490    8   41   63    0  18  12   
WT       345   311    50  2675   298    26   95  823   32   98    0  28   8   
d5        24    55     2     0     9     8   29   20  765    4    0   3  47   
d8       293   258     4     0     4    21  471    7   93   37    0   5  13   
dAD      294   363  3302     1   116     8   92   29   38   56    0  10  13   
dID      356   389    27    11   103  2523  109   64   46  288    0  51  13   
dVWRPY   152   215    94    74  2141    32   40  825   48   41    0  21  17   

leiden  13  14  
group           
Base    26   5  
Naive    0   0  
Null    23   8  
WT      18  23  
d5       2   1  
d8       1   2  
dAD     17  12  
dID     17  14  
dVWRPY   8  23  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7    8    9   10   11  12  \
group                                                                          
Base    1384  1259     5    27     1     7  725   20  505   29  169    0  32   
Naive      0     0     0     0     0     0    0    0    1    0    0  542   0   
Null    2214  1366    25     6     0     4  464    5  316   44   62    0  17   
WT       306   224    47   347  2548    25   84  904  142   32   95    0  28   
d5        24    26     3     9     0     8   25   20   33  765    3    0   3   
d8       248   186     1     6     0    19  411    5  194   85   33    0   5   
dAD      254   292  3214   118     1     8   84   27  218   37   46    0  10   
dID      304   309    19    95    11  2506   91   59  200   50  283    0  41   
dVWRPY   133   122    85  2215    54    28   33  773  130   50   40    0  21   

leiden  13  14  15  
group               
Base     3  25   6  
Naive    1   0   0  
Null    12  23   7  
WT       8  18  22  
d5      47   2   1  
d8      13   1   2  
dAD     13  17  12  
dID     13  17  13  
dVWRPY  16   8  23  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:15)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7    8    9   10  11  12  \
group                                                                         
Base    1366     6  1280     6    26     6  791  452   24  169    0  32  27   
Naive      0     0     0     0     0     0    0    1    0    0  542   0   0   
Null    2170     3  1434    25     4     4  512  243   45   61    0  17  23   
WT       294  3412   242    48   338    26   95  138   31  106    0  28  33   
d5        21    17    31     3    12     7   28   32  763    4    0   5   2   
d8       236     1   198     4     8    14  464  155   74   33    0   5   1   
dAD      251    12   272  3326   124     6   98  116   37   45    0   9  19   
dID      288    39   332    22   103  2473  118  178   45  291    0  51  37   
dVWRPY   119   653   140    93  2312    33   40  147   48   43    0  21  16   

leiden  13  14  
group           
Base     9   3  
Naive    0   1  
Null    13  11  
WT      31   8  
d5       1  43  
d8       4  12  
dAD     23  13  
dID     23  11  
dVWRPY  50  16  
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())

35 PCs, neigbhor 3 to 18¶

InĀ [7]:
iterate_neighbors(adata, pcs = 35, neighbors = 3, min = 0, max = 18)
computing neighbors
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 48 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:02)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3    4    5     6     7    8    9  ...  38  39  \
group                                                          ...           
Base       8     8   25    12  198  436     5     0  244  405  ...   3  44   
Naive      0     0    0     0    0    0     0     0    0    0  ...   1   0   
Null       3    29    4     0  677  481    40     0  563  263  ...  11   7   
WT        37    25  156  1052   43   56    27  1127   38   45  ...   8   7   
d5         2     0    6     0    2    5     2     0    6   19  ...  32  10   
d8        13     0    6     4   91   40     0     0   82  248  ...  11   8   
dAD        4  1317   76     4   98   61  1041     0   93   44  ...  13   3   
dID     1592    14   51    34   59   56    19     2   74   60  ...  10   3   
dVWRPY    34    65  928   102   22   42    43     9   34   28  ...  16   2   

leiden  40  41  42  43  44  45  46  47  
group                                   
Base     0   0   0   0   0   0   0   0  
Naive    0   0   0   0   3   0   0   0  
Null     0   0   4   0   0   0   0   0  
WT       0   0   0   0   0   1   0   0  
d5      81   7   0   4   0   0   0   1  
d8       0   0   0   0   0   0   0   1  
dAD      0   0   0   0   0   0   0   0  
dID      0   0   0   0   0   1   0   1  
dVWRPY   0   1   0   0   0   1   3   0  

[9 rows x 48 columns]
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 24 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4    5    6     7    8    9  ...   14   15  \
group                                                          ...             
Base     826     4    13  679     9  614  558    21   19   54  ...  189  135   
Naive      0     0     0    0     0    0    0     0    0    0  ...    0    0   
Null    1526     0    46  710     3  972  479     1    6   15  ...   65   31   
WT       135  2646    34  173    45   91   64   258  506  130  ...  110  299   
d5        10     2     2   44     3    9   18     6   14    4  ...    7   17   
d8       142     0     2  145    17  153  310     4   10   12  ...   31   10   
dAD      204     3  2397  248     6  122   80    37   37  122  ...   59   44   
dID      132    16    25  200  2115  153  106    50   60   58  ...  317  181   
dVWRPY    81    74    61  137    44   71   34  1188  855  853  ...   47   43   

leiden   16   17  18  19  20  21  22  23  
group                                     
Base      0    3  35  33   3  22   0   8  
Naive   542    0   0   0   1   0   0   0  
Null      0    3  25  18  11  17   0  17  
WT        0    5  76  28   8  25   0   4  
d5        0    1   8   3  47   1  93   1  
d8        0    2   6   5  12   1   0   0  
dAD       0    2  29   9  13  12   0   3  
dID       0  242  29  47  11  16   0   6  
dVWRPY    0    3  46  20  16   5   2   0  

[9 rows x 24 columns]
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 20 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4     5     6    7    8    9   10   11   12  \
group                                                                           
Base      11  1039    15  994     7   404    12   58  441  461   28  182  369   
Naive      0     0     0    0     0     0     0    0    1    0    0    0    0   
Null      42  1463     0  824     4  1282     2   23  263  266   48   85  174   
WT        45   149  2997  227    37    83   360  180   67   95   32  115   35   
d5         3    17     8   44     7     5    10    8   18   17  659    5   10   
d8         3   141     0  174    14   160    13   11  275  231   95   30   34   
dAD     3010   171     4  432    10   177    53  180   60   50   39   57   26   
dID       28   148    41  242  2421   159    55   96  126   70   49  305   35   
dVWRPY    79    68   127  248    43    73  1743  986   32   45   49   42   11   

leiden   13   14  15  16  17  18  19  
group                                 
Base    117    0   4  30   3  22   0  
Naive     0  542   0   0   1   0   0  
Null     39    0   5  17  11  17   0  
WT      253    0  99  28   8  20   0  
d5       19    0   5   3  39   1  91  
d8        9    0   1   5  12   1   0  
dAD      42    0   1  10  13  16   0  
dID     133    0  18  56  11  18   0  
dVWRPY   45    0  94  19  16  10   1  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 17 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10   11  \
group                                                                       
Base    1089    15    11  1011  1164    26    10  412   26   35  174  166   
Naive      0     0     0     0     1     0     0    0    0    0    0    0   
Null    1688    49     1   933   723     6     4  941    8   46   62   59   
WT       187    50  3070   180   117   320    42   68  304   33  113  283   
d5        18     2     1    49    29    11     5    6   18  660    4   22   
d8       168     3     0   226   502     9    20  120    7   89   32   15   
dAD      209  3149     4   283   125   105    10  151  136   32   47   61   
dID      172    31    30   255   158    77  2308  132   64   49  461  194   
dVWRPY    98    98   126   128    55  2060    43   75  822   54   42   82   

leiden   12  13  14  15   16  
group                         
Base      0  30  24   4    0  
Naive   542   0   0   1    0  
Null      0  17  17  11    0  
WT        0  27  28   8    0  
d5        0   3   2  39  100  
d8        0   5   1  12    0  
dAD       0  10  16  13    0  
dID       0  50  19  11    0  
dVWRPY    0  20  11  16    1  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4     5     6     7    8    9   10   11  \
group                                                                       
Base    1016    10     7  946    22  1113   654    11   31   15  191  124   
Naive      0     0     0    0     0     1     0     0    0    0    0    0   
Null    1667    42     0  771     8   634  1227     6   43    6   65   48   
WT       175    47  3057  252   327   109    93    37   38  256  116  264   
d5        19     2     2   46    11    26    15     7  765   11    3   19   
d8       137     0     1  214     9   485   184    21   90    5   33   12   
dAD      229  3082     4  442   124   107   168     8   35   17   50   46   
dID      178    26    16  274    87   151   153  2459   50   55  296  194   
dVWRPY    90    84   124  205  2234    56    89    33   54  597   41   81   

leiden   12  13  14  15  
group                    
Base      0  31   3  23  
Naive   542   0   1   0  
Null      0  17  11  20  
WT        0  28   8  23  
d5        0   3  39   1  
d8        0   5  12   1  
dAD       0  10  13  16  
dID       0  43  11  18  
dVWRPY    0  20  16   7  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10   11  12  \
group                                                                           
Base    1118    12     7    26   838  1117     9  691   28  119  173    0  31   
Naive      0     0     0     0     0     0     0    1    0    0    0  542   0   
Null    1874     3    26     4  1234   809     2  410   46   43   60    0  17   
WT       178  3233    43   379   140   115    44  211   32  284  108    0  29   
d5        18    10     2    14    27    26     7   32  764   21    3    0   3   
d8       200     2     0    11   180   432    16  223   85   10   31    0   5   
dAD      247     6  3023   117   271   131    11  370   37   47   48    0  10   
dID      193    36    26    84   196   131  2463  250   47  205  277    0  57   
dVWRPY   102   297    91  2551   121    55    37  259   54   74   41    0  20   

leiden  13  14  
group           
Base    26   2  
Naive    0   1  
Null    26  11  
WT      26   8  
d5       1  41  
d8       1  13  
dAD     20  13  
dID     35  11  
dVWRPY  13  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5     6    7    8    9   10  11  12  \
group                                                                         
Base    1350    15  1490     9    33  881     8   34  184  134    0  30  26   
Naive      0     0     1     0     0    0     0    0    0    0  542   0   0   
Null    2411     3  1036    38     7  849     4   43   77   43    0  17  26   
WT       224  3302   123    48   401  253    42   37   95  241    0  30  26   
d5        20    12    28     2    13   46     7  770    5   19    0   3   1   
d8       262     2   558     3    13  202    17   95   31    7    0   5   1   
dAD      284     7   157  3193   121  406    10   38   54   40    0  10  18   
dID      271    45   180    27    93  286  2506   49  284  182    0  43  34   
dVWRPY   140   314    67   101  2597  272    47   53   37   54    0  20  13   

leiden  13  
group       
Base     3  
Naive    1  
Null    11  
WT       8  
d5      43  
d8      13  
dAD     13  
dID     11  
dVWRPY  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4     5     6    7    8    9   10   11  12  \
group                                                                          
Base    1289  1572     8    10  831    20    40   32   16  133  186    0  30   
Naive      0     1     0     0    0     0     0    0    0    0    0  542   0   
Null    2445  1048    36     0  788     9    10   46    8   44   76    0  17   
WT       207   130    46  3052  244   328    48   36  296  280   98    0  30   
d5        22    29     1     1   48    11     6  771   11   21    3    0   3   
d8       264   545     3     0  198     7    27   99    6    8   33    0   5   
dAD      299   155  3148     1  402   124    11   39   28   47   56    0  10   
dID      264   184    24    18  255    84  2504   51   60  192  288    0  43   
dVWRPY   118    70    92   124  230  2149    34   52  701   73   38    0  20   

leiden  13  14  
group           
Base    27   3  
Naive    0   1  
Null    27  11  
WT      27   8  
d5       1  41  
d8       1  13  
dAD     18  13  
dID     33  11  
dVWRPY  14  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10  11  12  \
group                                                                          
Base    1236  1623    12   877     5    29    24   27  202  102    0  30  27   
Naive      1     0     0     0     0     0     0    0    0    0  542   0   0   
Null    1113  1266     3  1916    38    10     6   46   79   35    0  17  25   
WT       310   159  3334   155    46   335    53   36  101  232    0  27  34   
d5        57    29    11    17     1    14     6  762    5   21    0   3   0   
d8       265   514     2   206     1    11    46   97   39    8    0   6   2   
dAD      645   155     5   226  3007   124    10   35   57   46    0  10  18   
dID      340   159    37   232    23    93  2514   48  296  166    0  54  38   
dVWRPY   436    80   338    99    87  2447    40   54   39   61    0  20  14   

leiden  13  
group       
Base     3  
Naive    1  
Null    11  
WT       8  
d5      43  
d8      12  
dAD     13  
dID     11  
dVWRPY  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7    8    9   10  11  12  \
group                                                                         
Base    1463  1345    13    28     5     7  962   29  184  100    0  27  31   
Naive      0     0     0     0     0     0    1    0    0    0  542   0   0   
Null    2395  1379     0     9    27     4  550   41   71   35    0  26  17   
WT       212   304  3332   357    42    49   94   29  112  227    0  38  26   
d5        21    61     9    15     2     7   25  761    5   18    0   1   3   
d8       262   278     1    12     1    15  486   94   32    8    0   2   5   
dAD      263   936     4   124  2750     9  100   35   56   34    0  18   9   
dID      255   361    42   100    25  2514  130   50  288  154    0  39  42   
dVWRPY   137   252   187  2791    94    31   45   52   40   50    0  16  20   

leiden  13  
group       
Base     3  
Naive    1  
Null    11  
WT       8  
d5      41  
d8      13  
dAD     13  
dID     11  
dVWRPY  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:08)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5     6     7    8    9   10   11  12  \
group                                                                           
Base    1439  1332     7     6     8  989    28    26   32  178   91    0  28   
Naive      0     0     0     0     0    1     0     0    0    0    0  542   0   
Null    1451  2270     0    36     4  590     8     7   43   66   36    0  26   
WT       282   185  3117    40    38   98   283   359   31  104  222    0  35   
d5        61    19     2     1     6   28     8    11  764    4   19    0   1   
d8       291   234     0     1    12  497     8     9   95   33    9    0   2   
dAD      679   237     1  2988     7  111    94    67   32   56   38    0  18   
dID      357   221    26    26  2504  132    74    78   53  289  163    0  34   
dVWRPY   205   112   121    70    22   43  1789  1161   49   39   60    0  24   

leiden  13  14  
group           
Base    30   3  
Naive    0   1  
Null    17  11  
WT      28   8  
d5       3  42  
d8       5  13  
dAD     10  13  
dID     43  11  
dVWRPY  20  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10  11  12  \
group                                                                          
Base    1242  1296    16  1252     4    26    16   30  155   99    0  30  28   
Naive      0     1     0     0     0     0     0    0    0    0  542   0   0   
Null    2368  1196     4   771    28     7     6   45   55   29    0  17  28   
WT       201   290  3363   123    42   356    46   32  105  201    0  30  33   
d5        18    63     9    31     0    13     6  765    4   16    0   3   1   
d8       246   267     2   500     0    11    28  101   28    6    0   6   2   
dAD      262   865    13   121  2818    98     9   37   47   36    0  10  22   
dID      258   339    55   142    21    86  2515   51  283  157    0  58  35   
dVWRPY   122   311   637    60    82  2283    33   52   40   58    0  21  16   

leiden  13  
group       
Base     3  
Naive    1  
Null    11  
WT       8  
d5      40  
d8      12  
dAD     13  
dID     11  
dVWRPY  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:10)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10  11  12  \
group                                                                          
Base    1371  1187    12    24     6  1180    18   32  187  120    0  30  26   
Naive      1     0     0     0     0     0     0    0    0    0  542   0   0   
Null    1287  2179     2    11    36   833     6   45   73   41    0  17  24   
WT       264   194  3350   358    45   119    44   34   96  261    0  26  31   
d5        56    19    10    14     1    31     6  762    4   19    0   3   3   
d8       287   217     1     9     1   507    31   93   34   10    0   5   2   
dAD      675   237     3   126  3006   130     9   32   50   42    0  10  18   
dID      347   244    43    81    20   150  2503   51  285  183    0  55  38   
dVWRPY   227   126   302  2694    84    60    27   52   39   68    0  22  14   

leiden  13  
group       
Base     4  
Naive    1  
Null    11  
WT       8  
d5      41  
d8      12  
dAD     13  
dID     11  
dVWRPY  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:09)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10  11  12  \
group                                                                          
Base    1419  1070    11    25     4  1191    91   29  183  116    0  30  26   
Naive      1     0     0     0     0     0     0    0    0    0  542   0   0   
Null    1370  2119     0     7    27   839    12   44   64   32    0  17  23   
WT       279   186  3364   373    50   125    34   28  110  219    0  26  28   
d5        65    17     8    15     2    29     6  766    4   19    0   3   1   
d8       293   198     1    10     0   485    71   94   31    7    0   5   2   
dAD      673   244     3   112  2998   133    16   36   55   39    0  10  19   
dID      348   236    51   104    20   167  2472   51  303  159    0  55  34   
dVWRPY   212   120   177  2832    88    60    35   50   41   65    0  21  14   

leiden  13  
group       
Base     2  
Naive    1  
Null    11  
WT       8  
d5      34  
d8      12  
dAD     13  
dID     11  
dVWRPY  16  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:09)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10   11  12  \
group                                                                           
Base    1193  1398     6     3  1150    10    27   21   30  186  113    0  27   
Naive      0     1     0     0     0     0     0    0    0    0    0  542   0   
Null    2371  1259    31     0   679     7    11    4   44   63   42    0  26   
WT       178   263    48  3108   110    41   297  340   31  101  247    0  30   
d5        18    68     1     2    28     5    10   14  763    4   18    0   1   
d8       247   276     0     0   495    16     8    9   96   35    8    0   2   
dAD      261   506  3135     1   121    10   107   41   34   56   37    0  19   
dID      265   328    19    22   141  2512    74   64   49  286  163    0  35   
dVWRPY   111   194    82   142    56    27  1947  964   53   38   60    0  23   

leiden  13  14  
group           
Base    31   2  
Naive    0   1  
Null    17  11  
WT      28   8  
d5       3  34  
d8       5  12  
dAD     10  13  
dID     42  11  
dVWRPY  20  14  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:08)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10  11  12  \
group                                                                          
Base    1215  1411    10    10    19  1138     9   28  182  116    0  27  30   
Naive      0     1     0     0     0     0     0    0    0    0  542   0   0   
Null    2313  1226     0    35     9   779     3   45   61   43    0  23  17   
WT       213   279  3346    56   345   118    33   30   95  241    0  39  27   
d5        20    65     8     1    16    26     6  768    4   18    0   1   3   
d8       254   290     1     0    10   485    13   93   35    9    0   2   5   
dAD      263   435     3  3250   109   121    10   35   45   38    0  19  10   
dID      270   354    36    27    86   129  2502   49  283  184    0  37  43   
dVWRPY   137   222   188    99  2771    61    37   52   37   68    0  24  20   

leiden  13  
group       
Base     2  
Naive    1  
Null    11  
WT       8  
d5      33  
d8      12  
dAD     13  
dID     11  
dVWRPY  15  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10  11  12  \
group                                                                          
Base    1419   945  1400     8    18     8     7   30  197  106    0  27  30   
Naive      1     0     0     0     0     0     0    0    0    0  542   0   0   
Null    1196  1965  1145     0    11    32     3   46   77   38    0  24  17   
WT       285   175   150  3361   351    49    37   33   99  217    0  38  27   
d5        62    17    30     8    15     0     5  768    4   22    0   1   3   
d8       323   195   510     1    11     0    12   93   37    7    0   2   6   
dAD      472   236   174     3   124  3169     9   34   47   41    0  19  10   
dID      366   225   164    38    88    25  2509   49  281  165    0  38  52   
dVWRPY   217   127    80   180  2784    91    34   54   37   67    0  24  21   

leiden  13  
group       
Base     2  
Naive    1  
Null    11  
WT       8  
d5      34  
d8      12  
dAD     13  
dID     11  
dVWRPY  15  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10  11  12  \
group                                                                          
Base    1463    13   876  1437    20     6     7   25  188  103    0  27  30   
Naive      1     0     0     0     0     0     0    0    0    0  542   0   0   
Null    1214     2  1933  1175    10    26     3   46   64   39    0  25  17   
WT       278  3356   162   153   377    45    30   34   99  222    0  38  28   
d5        60    10    17    32    16     0     5  767    4   20    0   1   3   
d8       327     2   189   514    10     0    14   90   35    8    0   2   6   
dAD      599     3   220   169   122  3060     7   34   54   41    0  19  10   
dID      355    50   227   174    81    25  2479   48  291  179    0  39  52   
dVWRPY   245   304   114    77  2657    88    28   54   41   69    0  18  21   

leiden  13  
group       
Base     2  
Naive    1  
Null    11  
WT       8  
d5      34  
d8      12  
dAD     13  
dID     11  
dVWRPY  15  
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())

40 PCs, neigbhor 3 to 18¶

InĀ [8]:
iterate_neighbors(adata, pcs = 40, neighbors = 3, min = 0, max = 18)
computing neighbors
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 51 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:02)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7     8    9  ...  41  42  \
group                                                            ...           
Base      13    10     2    11    15    15  180  444    10  412  ...   0   7   
Naive      0     0     0     0     0     0    0    0     0    0  ...   0   0   
Null      40     4     0     0    21     6  688  510     4  221  ...   0   4   
WT        29   250  1410  1088    20    47   56   57    20   62  ...   0  29   
d5         2    10     6     3     1     8    4    5     5   12  ...  93   0   
d8         3     3     1     2     2     9   52   32     9  244  ...   0   1   
dAD     1415    30     0     6  1126     7  120   54     5   39  ...   0   8   
dID       22    29     5    32    11  1121   87   38  1001   34  ...   0  19   
dVWRPY    57  1197    49   125    38    18   35   25    25   32  ...   1   9   

leiden  43  44  45  46  47  48  49  50  
group                                   
Base    38   0   1   2   0   0   0   0  
Naive    0   0   0   0   0   3   0   0  
Null    19   0   0   6   0   0   0   0  
WT       4   0  11   0   0   0   0   0  
d5       2  23   0   0   7   0   0   0  
d8       1   0   0   0   0   0   0   0  
dAD      4   0   0   0   0   0   0   0  
dID      4   0   0   1   0   0   3   3  
dVWRPY   4   0   4   0   1   0   0   0  

[9 rows x 51 columns]
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 28 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3     4    5    6     7    8    9  ...   18   19  \
group                                                          ...             
Base      12    12  605    10     9  477  347     4   36  692  ...    0    1   
Naive      0     0    0     0     0    0    0     0    0    0  ...  542    0   
Null       0     0  872    62    32  571  796     0   10  403  ...    0    1   
WT      2789    42   90    32    21   85   56   249  286   57  ...    0    2   
d5         7     9    7     4     1   22   26     6   16    5  ...    0    1   
d8         0    23   66     6     2   92  105     5   14   83  ...    0    0   
dAD        3     9   88  1529  1565  202  149    40   90   60  ...    0    1   
dID       36  2083   48    50     4  141  105    38   73   51  ...    0  215   
dVWRPY   118    29   42    58    49   87   49  1262  992   31  ...    0    1   

leiden  20  21   22  23  24  25  26  27  
group                                    
Base    32   8    1   3  15  13   0   1  
Naive    0   0    0   1   0   0   0   0  
Null    17  11    0  11  13  16   0   1  
WT      26  49  129   8  32  19   0   6  
d5       9   2    0  41   1   0  28   0  
d8       6   7    0  12   2   1   0   0  
dAD     11  24    1  13   5   8   0   2  
dID     49  21    2  10  10  13   0   5  
dVWRPY  26  54   41  15  11   4   0   4  

[9 rows x 28 columns]
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 21 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3     4     5    6    7    8     9  ...   11   12  \
group                                                           ...             
Base      10    14  922   950    13    19  634  344  650    13  ...   29  198   
Naive      0     0    0     0     0     0    1    0    0     0  ...    0    0   
Null      44     0  893  1157     4     7  409  784  383     4  ...   47   64   
WT        42  2886  193   131    50   269  126   63   68   348  ...   37  110   
d5         3     6   33    14    11     4   32   15   17    17  ...  751    3   
d8         4     1  136   139    13    12  256   93  332     7  ...   96   36   
dAD     3030     4  328   168     4    84  172  154   62    71  ...   37   53   
dID       30    28  184   111  2146    66  241  155   77    62  ...   51  305   
dVWRPY    95   102  213    86    36  1616   94   71   27  1087  ...   49   38   

leiden   13   14   15   16  17  18  19  20  
group                                       
Base    123    0   12    1  31  22   3  17  
Naive     0  542    0    0   0   0   1   0  
Null     20    0    8    0  17  20  11  14  
WT      268    0    3  112  24  27   8  32  
d5       19    0    0    0   9   0  33   1  
d8        9    0    1    0   3   1  12   2  
dAD      44    0    0    3   9  16  13   5  
dID     169    0  225    2  43  41  11   8  
dVWRPY   79    0    1   48  24  11  15  12  

[9 rows x 21 columns]
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 19 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6     7    8    9   10   11  \
group                                                                       
Base    1128     6  1192    10    16    20  678     9  338   28  333  105   
Naive      0     0     0     0     0     0    0     0    1    0    0    0   
Null    1628    50  1106     0     5     7  712     5  196   46  214  440   
WT       191    44   157  3045    50   260   80   238  242   30   39   28   
d5        15     5    29     6     9     5   18    12   38  742   14    4   
d8       184     4   164     1    13    11  286     9   97   95  232   53   
dAD      234  3160   288     6     3    80  101    69  123   34   45   72   
dID      194    40   195    33  2384    68   92    62  133   49  128   83   
dVWRPY   129   107   149   150    34  1696   33  1026  152   47   23   27   

leiden   12   13   14  15  16  17  18  
group                                  
Base    176   83    0  32  24   3  16  
Naive     0    0  542   0   0   1   0  
Null     67   24    0  17  22  11  15  
WT      122  212    0  24  28   8  32  
d5        3   19    0   3   0  47   0  
d8       34    6    0   5   1  12   2  
dAD      49   49    0  11   9  13   5  
dID     294  154    0  48  34  12   8  
dVWRPY   42   55    0  23  11  15  12  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 18 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5     6     7    8    9   10   11  \
group                                                                       
Base    1246  1226     9    12     9  914    23    18  251   30  179  195   
Naive      0     0     0     0     0    1     0     0    0    0    0    0   
Null    1989  1104    48     0     2  512     5     7  674   46   44   65   
WT       168   265    45  2890    46  100   324   417   45   29  289  119   
d5        16    50     1     4     7   25     7    16    9  758   23    3   
d8       185   197     1     1    14  520     9     6  109  101   13   32   
dAD      231   489  3102     2     5  104    66    68  106   32   51   52   
dID      170   270    34    25  2425  185    65    79  111   52  199  293   
dVWRPY   125   208   112   102    20   47  1689  1156   49   49   77   42   

leiden   12  13  14  15  16  17  
group                            
Base      0  28  24   3  17  13  
Naive   542   0   0   1   0   0  
Null      0  16  21  11  15   6  
WT        0  24  30   8  30   1  
d5        0   4   0  46   0   0  
d8        0   5   1  12   2   1  
dAD       0   9  15  13   6   0  
dID       0  44  35  12   8   4  
dVWRPY    0  16  12  15  12   0  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 17 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10   11  \
group                                                                       
Base    1073     5  1307     5   762    25     7  556   14   28  179  163   
Naive      0     0     1     0     0     0     0    0    0    0    0    0   
Null    1844    35   750     0  1267     6     2  416    6   43   47   87   
WT       156    44   126  2851   107   391    43  215  365   28  298  113   
d5        14     2    33     1    17    13     7   33    9  764   22    4   
d8       173     0   521     0   195    10    14  138    4   94   12   27   
dAD      217  2956   126     2   214   106     4  506   30   30   55   61   
dID      164    29   179    16   180    91  2426  215   48   47  214  287   
dVWRPY   111    98    60    88    88  2149    25  226  667   47   77   39   

leiden   12  13  14  15  16  
group                        
Base      0  28  25   3  17  
Naive   542   0   0   1   0  
Null      0  16  20  11  15  
WT        0  25  32   8  28  
d5        0   3   0  47   0  
d8        0   6   1  13   1  
dAD       0   9  16  13   6  
dID       0  56  39  12   8  
dVWRPY    0  16  13  15  12  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10   11  12  \
group                                                                           
Base    1465    16   991     3    25   919     9  373   28  189  105    0  30   
Naive      0     0     0     0     0     0     0    1    0    0    0  542   0   
Null    1143     2  1348    37     8  1581     4  213   39   90   35    0  16   
WT       133  3187   179    47   434   159    55  145   31  113  251    0  25   
d5        33     8    32     3    15    13     8   31  760    5   18    0   3   
d8       569     3   213     2     8   157    14   91   91   33    6    0   7   
dAD      156    10   336  3268   119   194     5   83   30   55   49    0  10   
dID      183    51   288    29    77   177  2470  112   48  290  168    0  57   
dVWRPY    64   270   151   111  2639   112    34  128   50   41   73    0  19   

leiden  13  14  15  
group               
Base    25   3  16  
Naive    0   1   0  
Null    23  11  15  
WT      31   8  32  
d5       0  39   1  
d8       1  13   1  
dAD     17  13   6  
dID     39  12  10  
dVWRPY  12  15  12  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10  11  12  \
group                                                                          
Base    1251    14     5    15  1175   743    14  665   29  198    0  30  26   
Naive      1     0     0     0     0     0     0    0    0    0  542   0   0   
Null    1097     0    39     4   965  1539     2  724   42   83    0  16  23   
WT       302  3228    43   357   126   108    54  366   31  113    0  25  36   
d5        57     6     1    14    23    12     8   28  767    6    0   3   0   
d8       274     1     0     7   490   142    22  120   95   35    0   5   2   
dAD      642     7  3026    87   129   161     6  156   33   58    0  10  17   
dID      336    40    22    85   133   150  2480  312   48  286    0  56  37   
dVWRPY   332   179   120  2630    54    71    35  161   50   41    0  19  13   

leiden  13  14  15  
group               
Base     3  18  11  
Naive    1   0   0  
Null    11  13   7  
WT       8  33   0  
d5      44   0   0  
d8      13   2   1  
dAD     13   6   0  
dID     12  11   3  
dVWRPY  15  11   0  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7    8    9   10  11  12  \
group                                                                         
Base    1550  1346    14    28     8    10  863   33  195    0   55  31  29   
Naive      0     1     0     0     0     0    0    0    0  542    0   0   0   
Null    2554  1206     2     6    30     4  523   43   91    0   28  17  27   
WT       246   328  3345   328    49    53   90   33  104    0  157  24  36   
d5        14    60    10    13     2    10   24  756    5    0   12   3   1   
d8       282   278     3    10     1    10  454  107   33    0    8   6   2   
dAD      287   829     9   125  2821     3   98   35   59    0   34  10  22   
dID      313   369    50    90    24  2481  114   50  290    0  113  58  34   
dVWRPY   147   386   329  2493    78    43   39   54   41    0   50  23  19   

leiden  13  14  15  
group               
Base     3  19  13  
Naive    1   0   0  
Null    11  16   7  
WT       8  29   0  
d5      59   0   0  
d8      13   1   1  
dAD     13   6   0  
dID     11  10   4  
dVWRPY  16  13   0  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7    8    9  10  11  12  \
group                                                                        
Base    1568  1379    13    25    11    15  894   27  183    0  26   6  31   
Naive      0     0     0     0     0     0    1    0    0  542   0   0   0   
Null    2458  1187     0     8    38     4  684   43   64    0  23  13  17   
WT       368   309  3264   402    53    51  103   29  112    0  32  45  25   
d5        32    54     6    14     0     9   28  770    5    0   1   3   3   
d8       281   257     1    10     0    14  492   97   34    0   1   4   5   
dAD      311   557     2   119  3083     6  111   34   56    0  21  22  10   
dID      393   352    37    91    25  2529  132   49  284    0  40  17  41   
dVWRPY   153   290   176  2715    98    35   50   52   43    0  21  50  19   

leiden  13  14  
group           
Base     3  16  
Naive    1   0  
Null    11  15  
WT       8  29  
d5      44   0  
d8      12   1  
dAD     13   6  
dID     11  10  
dVWRPY  16  13  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5     6     7    8    9   10  11  12  \
group                                                                          
Base    1488  1377    10     6    19  945    22    16   30  199    0  31  29   
Naive      0     1     0     0     0    0     0     0    0    0  542   0   0   
Null    2275  1238     0    38     3  792     5     3   44   89    0  17  24   
WT       364   308  3124    47    52  103   219   342   31  110    0  23  29   
d5        30    58     1     0     9   30     7    15  773    5    0   3   1   
d8       264   279     0     0    22  472     5     9   98   37    0   6   2   
dAD      271   624     4  3048     7  115    71    46   34   60    0  10  18   
dID      374   357    30    24  2511  125    86    43   49  286    0  54  34   
dVWRPY   141   264   137    88    34   45  1600  1231   51   42    0  19  14   

leiden  13  14  15  
group               
Base     6   2  17  
Naive    0   1   0  
Null    11  11  15  
WT      41   8  29  
d5       3  34   0  
d8       2  12   1  
dAD     24  13   6  
dID     16  11  11  
dVWRPY  38  14  13  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6     7    8    9   10  11  12  \
group                                                                           
Base    1329  1087  1426     4     5    13    34    29   30  157    0  32  28   
Naive      0     0     1     0     0     0     0     0    0    0  542   0   0   
Null    2301  1079   951    32     0     3     7     5   42   67    0  17  24   
WT       259   298   136    46  2579    47   344   877   31  102    0  23  25   
d5        24    59    32     0     0     8     9    15  773    4    0   4   1   
d8       247   238   547     1     0    11    10     8   96   28    0   6   1   
dAD      263   660   152  2958     0     3   115    46   32   55    0  10  21   
dID      309   363   182    23    14  2503    92    74   51  277    0  55  33   
dVWRPY   122   252    66    77    75    25  1883  1049   50   42    0  19  15   

leiden  13  14  15  
group               
Base     5   2  16  
Naive    0   1   0  
Null    10  11  16  
WT      37   8  18  
d5       3  37   0  
d8       2  13   1  
dAD     17  13   6  
dID     14  11  10  
dVWRPY  30  14  12  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6     7    8    9   10  11  12  \
group                                                                          
Base    1574  1377    10    10    30     2  901    21   30  160    0  31  27   
Naive      0     0     0     0     0     0    1     0    0    0  542   0   0   
Null    2502  1286    42     3     5     0  533     5   45   66    0  17  25   
WT       354   278    47    46  1185  2338   98   252   31   92    0  23  23   
d5        26    59     1     8    17     0   30     8  775    4    0   3   1   
d8       276   282     1    14     9     0  483     5   92   26    0   5   1   
dAD      276   563  3121     6    51     0   98    90   31   48    0  10  18   
dID      374   356    34  2525    71    12  118    69   52  272    0  54  39   
dVWRPY   138   241    85    32  1169    46   38  1796   52   37    0  19  15   

leiden  13  14  15  
group               
Base     6   2  16  
Naive    0   1   0  
Null    10  11  15  
WT      38   8  17  
d5       3  34   0  
d8       2  12   1  
dAD     20  13   6  
dID     16  11   8  
dVWRPY  37  14  12  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6     7    8    9   10  11  12  \
group                                                                           
Base    1286  1342     6  1181     4    12    32    28   31  195    0  30  27   
Naive      0     0     0     1     0     0     0     0    0    0  542   0   0   
Null    2167  1298    38   841     0     3     5     6   45   85    0  17  22   
WT       284   309    50   109  2634    52   292   851   30   97    0  22  28   
d5        21    58     1    32     0    10     7    16  779    4    0   3   1   
d8       241   288     1   496     0    12     9    11   95   33    0   5   2   
dAD      251   659  3010   123     1     5    86    55   31   58    0  10  22   
dID      293   409    17   146    15  2499    82    84   50  285    0  55  36   
dVWRPY   118   267    87    46    60    31  1774  1162   50   39    0  19  13   

leiden  13  14  15  
group               
Base     5   2  16  
Naive    0   1   0  
Null    11  11  16  
WT      36   8  28  
d5       3  34   0  
d8       3  12   1  
dAD     21  13   6  
dID     18  11  11  
dVWRPY  38  14  13  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6     7    8    9   10   11  12  \
group                                                                           
Base    1343  1262     5    11     2    30  887    23  352   28  177    0  32   
Naive      0     0     0     0     0     0    1     0    0    0    0  542   0   
Null    2400  1221    33     2     0     5  541     5  177   44   71    0  17   
WT       168   233    43    46  2399  1031   88   288  339   30   94    0  23   
d5        17    49     1     8     0    18   27     8   23  777    4    0   3   
d8       254   270     0    14     0    10  466     6   42   96   31    0   5   
dAD      232   792  2879     4     0    61   96    82   75   30   53    0  10   
dID      204   310    37  2489    11    87  112    69  254   49  279    0  55   
dVWRPY   103   242    75    31    55  1192   36  1745  102   57   36    0  19   

leiden  13  14  15  
group               
Base    27   2  16  
Naive    0   1   0  
Null    24  11  14  
WT      22   8  18  
d5       1  33   0  
d8       2  12   1  
dAD     18  13   6  
dID     36  11   8  
dVWRPY  12  14  12  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4     5     6    7    8    9   10   11  12  \
group                                                                          
Base    1515    19   916     4  582    20    15  766   26  178   78    0  31   
Naive      0     0     0     0    0     0     0    1    0    0    0  542   0   
Null    1546     2  1684    30  631     7     3  456   48   61   31    0  17   
WT       145  3284   150    44  265   348    49   89   33  100  231    0  22   
d5        19     8    13     1   47    12     9   26  773    5   19    0   3   
d8       232     2   170     0  165     8    13  465   95   30    8    0   5   
dAD      165     6   208  2920  689   104     4   92   31   51   34    0  10   
dID      184    42   192    23  276    87  2485  124   49  296  139    0  54   
dVWRPY    86   279   104    81  447  2433    35   49   54   39   61    0  19   

leiden  13  14  15  
group               
Base    27   2  18  
Naive    0   1   0  
Null    23  11  15  
WT      33   8  29  
d5       1  33   0  
d8       3  12   1  
dAD     18  13   6  
dID     38  11  11  
dVWRPY  17  14  13  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:10)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10  11  12  \
group                                                                          
Base    1349  1034  1465     3     4    16    18   24   28  174    0  30  28   
Naive      0     0     1     0     0     0     0    0    0    0  542   0   0   
Null    2363  1016   970    19     0     2     6    6   44   66    0  17  23   
WT       362   264   130    39  2533    48   285  923   31  110    0  22  19   
d5        28    57    30     0     0     8     9   13  769    5    0   3   1   
d8       263   230   542     0     0    11     6    9   96   30    0   5   1   
dAD      293   820   150  2809     0     2   101   26   31   51    0  10  22   
dID      377   345   175    18    14  2500    66   70   47  281    0  48  37   
dVWRPY   148   307    60    73    73    25  1882  987   46   40    0  19  14   

leiden  13  14  15  
group               
Base     3   6  15  
Naive    1   0   0  
Null    11   9  13  
WT       8  30  26  
d5      45   1   0  
d8      13   2   1  
dAD     13  17   6  
dID     11  14   8  
dVWRPY  16  28  13  
computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5     6    7    8    9   10   11  12  \
group                                                                           
Base    1163  1139  1488     3    10    16    24   27   27  174    0   50  31   
Naive      0     0     1     0     0     0     0    0    0    0  542    0   0   
Null    1263  2125   939    25     0     2     8    6   44   64    0   25  17   
WT       286   190   133    45  2803    42   306  638   33  109    0  161  22   
d5        56    14    34     1     0     8    11   15  768    5    0   19   3   
d8       269   213   544     0     0    13     8   10   93   33    0    7   5   
dAD      825   241   148  2825     1     6   111   29   36   52    0   27  10   
dID      368   244   169    17    20  2523    85   61   47  281    0  116  41   
dVWRPY   301   106    59    71    96    26  2030  842   48   41    0   52  19   

leiden  13  14  15  
group               
Base    27   2  16  
Naive    0   1   0  
Null    21  11  15  
WT      20   8  34  
d5       1  34   0  
d8       1  12   1  
dAD     21  13   6  
dID     20  11   8  
dVWRPY  13  14  13  
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
InĀ [9]:
# End of Notebook
print("\nNotebook Ends")
Notebook Ends